The Prime Minister Tony Abbott has refused to confirm the comments, saying he would not negotiate the issue with Indonesia through the media.

"One of the things I am not going to do, and one of the things no government should do, if it wants to get the best possible outcome for the Australian people is engage in negotiations with another country, dare I say, through the media," he said.

When asked about the comments today, Foreign Affairs Minister Julie Bishop said: "I'm not going to go into the details. I suggest you talk to the Minister for Immigration."

Senior Government frontbencher Christopher Pyne says he has not been told of any such talks.

"I'm not aware of any people swap negotiations. But if there are any, I'm sure they'll be revealed at the appropriate time."

Labor frontbencher Chris Bowen says the Government needs to be upfront with the community if it is considering an asylum seeker swap deal.

"The previous government negotiated an arrangement with a country in our region, Malaysia. This Government was very critical of that," he said.

"If they're currently contemplating something similar to what they previously excoriated, then they would need to be upfront with the Australian people about that."

Indonesia's 'position on asylum seekers clear'

Meanwhile, a senior Indonesian government minister says he has made his country's position on asylum seekers clear, having already said Indonesia would not agree to Australia's policies.

Indonesia disputes whether the boat off Java last week was within its search and rescue zone.

During last week's standoff, Djoko Suyanto, the Indonesian coordinating minister for security and political affairs, seemed frustrated with Australia's requests.

In a text message to the ABC, Mr Suyanto said Indonesia had "never agreed" to Australia's policies on asylum seeker returns and that they should be sent to Australian detention centres "not" back to Indonesia.

When asked for an interview on Monday, he said: "I've said enough. It's clear where Indonesia's position is at and what our policy is."

Indonesia's foreign affairs minister has clarified that unless there is a risk to people's lives at sea, there is no reason for them to be returned to Indonesia.